Climate change in recent decades has been identified as a significant threat to natural environments and human wellbeing. This is because some of the contemporary changes to climate are abrupt and result in persistent changes in the state of natural systems; so called regime shifts (RS). This study aimed to detect and analyse the timing and strength of RS in Estonian climate at the half-century scale (1966-2013). We demonstrate that the extensive winter warming of the Northern Hemisphere in the late 1980s was represented in atmospheric, terrestrial, freshwater and marine systems to an extent not observed before or after the event within the studied time series. In 1989, abiotic variables displayed statistically significant regime shifts in atmospheric, river and marine systems, but not in lake and bog systems. This was followed by regime shifts in the biotic time series of bogs and marine ecosystems in 1990. However, many biotic time series lacked regime shifts, or the shifts were uncoupled from large-scale atmospheric circulation. We suggest that the latter is possibly due to complex and temporally variable interactions between abiotic and biotic elements with ecosystem properties buffering biotic responses to climate change signals, as well as being affected by concurrent anthropogenic impacts on natural environments.